The kidney comprises multiple cell types of both epithelial and mesenchymal origin, with highly defined regional subdivisions in the ductal systems. A full understanding of kidney development requires that each cell type can be uniquely identified by specific molecular markers. To this end, Andrew McMahon and colleagues have undertaken a comprehensive analysis of the RNA expression patterns of nearly one-thousand transcription factors in the embryonic mouse kidney (p. 1863). Their results not only identify novel markers, but also reveal an unexpected degree of restriction in expression of many factors, suggesting that anatomically defined compartments may be further subdivided at the molecular level. Moreover, this in situ dataset provides a starting point to understand the transcriptional networks underlying cell type specification. As proof of principle, the authors use published microarray and expression data to bioinformatically identify putative targets of five transcription factors and to uncover potential network topologies. This valuable resource has been made available to the community via the GUDMAP database.

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